Knox removed her clothes in her bedroom prior to taking a shower. After taking a shower, she realized that she left her towels in her bedroom. She then did the bathmat shuffle from the bathroom to the bedroom. It's a mystery why she walked to the bathroom freely without her clothes, but needed the bathmat to shuffle back to her bedroom. It sounds more like the bathmat shuffle was related to an explanation for why there were missing footprints.
Email where Knox describes removing her clothing in her bedroom prior to the shower
http://themurderofmeredithkercher.com/Amanda_Knox's_Email_Home
From your link, she says she dried her feet on the mat, not that she shuffled it to her bedroom. Even if she did, well, I've done that when my feet were wet and I didn't want to get the floor wet which would mean dirtying another towel to clean up the wet floor after.
How would the bathmat keep footprints from showing up under luminol? It apparently didn't even smudge Rudy's shoe prints.